title: CoCl2 induced cytotoxicity is associated with dysregulated circRNAs expression

city: Guangzhou

first: Rui

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

summary: To investigate differentially expressed circRNAs in C2C12 myotubes with/without CoCl2 treatment, we used mouse circRNA microarray to examine the expression of circRNAs in C2C12 myotubes and C2C12 myotubes with CoCl2 treatment.

overall_design: Cells from cell line C2C12 were distributed into two experimental groups:  CoCl2 group and control group, then perform circRNAs chips by Arraystar mouse circRNAs chip. Three independent experiments were performed at each group.

first: Yanling

last: She


title: CoCl2 induced cytotoxicity is associated with dysregulated lncRNAs expression

status: Public on May 28 2021

country: China

summary: To investigate differentially expressed lncRNAs in C2C12 myotubes with/without CoCl2 treatment, we used mouse lncRNA microarray to examine the expression of lncRNAs in C2C12 myotubes and C2C12 myotubes with CoCl2 treatment.

overall_design: Cells from cell line C2C12 were distributed into two experimental groups: CoCl2 group and control group, then perform lncRNAs chips by Arraystar mouse lncRNAs chip. Three independent experiments were performed at each group.


title: RNA sequencing of laser captured hippocampal deep and superficial CA1 subfields in epilepsy

city: San Joan d'Alacant

first: Jose

middle: P

last: Lopez-Atalaya

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias

country: Spain

institute: CSIC-UMH

type: Expression profiling by high throughput sequencing

summary: We profiled total mRNA of laser captured microdissected hippocampal deep and superficial CA1 subfields from adult male (45-50 days) Wistar rats (Rattus norvegicus) (180-200g) subjected to kainic acid-induced status epilepticus (chronic epileptic phase) and control animals.

overall_design: Adult male Wistar rats were subjected to kainic acid-induced status epilepticus or sham control (n = 3/group). RNA samples were collected after 6 to 8 weeks post-status when animals were in the chronic epileptic phase.

first: Alex

last: Bayes

first: Angel

last: Barco

first: Liset

last: Menendez de la Prida


title: Single-cell Transcriptomic Analysis Reveals Disparate Effector Differentiation Pathways in Human Treg Compartment

status: Public on May 27 2021

city: TianJin

first: Changlu

last: Xu

state: TianJin

address: 288 Nanjing Rd, Heping

department: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: A spatially-tracked single cell transcriptomics map of neuronal networks in the intrinsic cardiac nervous system

city: Philadelphia

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1020 Locust St, 314C

department: Pathology

country: USA

institute: Jefferson University


title: Single-cell Transcriptomic Analysis Reveals Disparate Effector Differentiation Pathways in Human Treg Compartment [Treg patients]

summary: Human FOXP3+ regulatory T (Treg) cells are central to immune tolerance. However, their heterogeneity and differentiation remain incompletely understood. Here we use single-cell RNA and T cell receptor sequencing to resolve Treg cells from healthy individuals and patients with or without acute graft-versus-host disease (aGVHD) who undergo stem cell transplantation. These analyses, combined with functional assays, separate Treg cells into naïve/activated/effector stages, and resolve the HLA-DRhi, LIMS1hi, highly suppressive FOXP3hi, and highly proliferative MKI67hi effector subsets. Trajectory analysis assembles Treg subsets into two differentiation paths (I/II) with distinctive phenotypic/functional programs, ending with the FOXP3hi and MKI67hi subsets, respectively. Transcription factors FOXP3 and SUB1 contribute to some Path I and Path II phenotypes, respectively. These FOXP3hi and MKI67hi subsets and two differentiation pathways are conserved in transplanted patients, despite having functional/migratory impairments under aGVHD. The findings expand the understanding of Treg cell heterogeneity and differentiation and provide a single-cell atlas for the dissection of Treg complexity in health and disease.

overall_design: Here, we performed droplet-based scRNA-seq of human FOXP3+ regulatory T (Treg) cells to construct a molecular landscape and dissecting the heterogeneity of Treg cells from healthy donors and transplanted patients with or without acute graft-versus-host disease (aGVHD).

first: Yuechen

last: Luo

first: Bing

last: Wang

first: Qing

last: Niu

first: Xiuhua

last: Su

first: Mingzhe

last: Han

first: Erlie

last: Jiang

first: Lihong

last: Shi

first: Xiaoming

last: Feng


title: Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis [II]

city: St. Louis

last: Rosenberg

state: MO

address: 660 S. Euclid Ave.

department: Molecular Microbiology

institute: Washington University in St. Louis

summary: During infection, Toxoplasma gondii translocate effector proteins directly into the infected host cells to subvert various immune signaling pathways. We identified a novel secreted effector-TgNSM that localizes to the host cell nucleus. Mechanistically, TgNSM drives increased NCoR/SMRT repressor complex levels and enhances transcriptional repression of interferon regulated genes (ISGs). Type I and type II interferons can induce necroptosis by upregulating protein kinase PKR that induces the formation of a necrosome complex consisting of the RIPK1 and RIPK3. The necrosome then activates the pro-necroptotic protein MLKL to execute necrotic cell death. TgNSM acts together with another secreted effector TgIST, previously shown to down-modulate IFN-γ signaling. TgNSM and TgIST block IFN driven expression of PKR and MLKL, thus preventing host cell necroptotic death and assuring survival of intracellular cysts. The mechanism of action of TgNSM highlights a previously unappreciated role of NCoR/SMRT in regulation of necroptosis.

overall_design: We created HeLa stable line expressing TgNSM-TY upon DOX treatment. For RNA seq experiments in HeLa cells, HeLa-tet and HeLa-tet-TgNSM-TY cell lines were seed at a density of 0.06x10e6 /ml in T25 flasks. The next day DOX (Sigma) was added to a final concentration of 1µg/ml. After 48 hr culture media was replaced for fresh DOX media ±IFNγ 100U/ml. Cells were collected 6 hr post ±IFNγ media swap and their RNA was extracted and sequenced using Illumina chemistry on a illumina NovaSeq 6000 using paired-end reads extending 150 bases. Three biological replicates were done for each sample.

first: L

middle: D

last: Sibley


title: Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis


title: Ras/ERK and PI3K/AKT signaling differentially regulate oncogenic ERG mediated transcription in prostate cells

city: Bloomington

first: Brady

middle: Guy

last: Strittmatter

state: IN

address: 1001 E Jordan Street

department: Molecular and Cellular Biochemistry

institute: Indiana University Bloomington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Ras/ERK and PI3K/AKT pathways differentially regulate the oncogene ERG in prostate cancer resulting in differential transcriptional profile

overall_design: ChIP-Sequencing of H3K27me3 in RWPE1 prostate cells expressing Vector, WT ERG, or phospho-mutant ERG-S96E. ChIP-Sequencing of ERK2 in RWPE1 and RWPE1-ERG cells.  ChIP-Sequencing of ERG in RWPE1 cells expressing myristolated AKT. RNA-Sequencing of polyA selected RNA from RWPE1 expressing Vector, mAKT, ERG, or ERG+mAKT.

middle: G

first: Peter

middle: C

last: Hollenhorst


title: Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells [scRNA-seq]

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

summary: Blood production is maintained through adult life by haematopoietic stem cells which undergo a process of differentiation and increasing lineage restriction to produce all the terminal blood types. The cell type transitions within this process are tightly controlled, and loss of control can lead to inappropriate proliferation and leukemic transformation. We and others have previously described seven transcriptional regulators (heptad; LYL1, TAL1, LMO2, FLI1, ERG, GATA2, RUNX1) which bind key haematopoietic genes in normal human CD34+ haematopoietic stem and progenitor cells (HSPCs). Heptad factors form a densely interconnected circuit by binding combinatorically at their own, and each other’s, regulatory elements. However, the precise role of the heptad throughout normal and leukemic haematopoiesis, including whether all seven factors act together in single cells, and whether heptad perturbation can influence cell fate decisions remain unclear. In this study we integrate bulk and single cell data in normal human HSPCs and leukemic cells and find that chromatin conformation at key heptad regulatory elements is predictive of cell identity in normal and leukemic progenitors. The interconnected heptad circuit identified in normal HSPCs persists in AML, but single cell transcriptomics suggest that specific heptad sub-circuits exist in individual cells, and we show that GATA2, TAL1 and ERG play key roles in regulating the stem to erythroid transition in both normal and leukemic contexts.

overall_design: Single cell RNAseq of unperturbed ME-1 AML cells (DSMZ cat# ACC 537)

first: John

last: Pimanda

first: Fabio

last: Zanini

first: Janith

last: Seneviratne


title: Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells [RNA-seq]

overall_design: RNAseq of primary human CD34+ HSPCs lentivirally transduced with shRNAs targetting luciferse (control) or ERG.


title: Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells [ChIP-seq]

overall_design: ChIPseq of transcription factors and histone modifications in ME-1 and KG-1 acute myeloid leukemia cells


title: Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells


title: Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis [I]

first: Alex

overall_design: We created single and double mutant strains in the type II (ME49) line (i.e. WT, ∆nsm, ∆ist and ∆nsm/∆ist)  carrying mCardinal (mCard) driven by a constitutive tubulin promoter and the bradyzoite specific promoter BAG1 driving mNeonGreen (mNG). The strains were grown in HFF cells under alkaline stress to induce T. gondii differentiation into bradyzoites for 5 days. Infected HFF monolayers were then stimulated with IFN-γ for 6 hr, harvested, and infected cells were purified by fluorescence-activated cell sorting (FACS) based on the expression of both mCard and mNG. RNA was then extracted and sequenced using Illumina chemistry on a NovaSeq-6000 using paired end reads extending 150 bases. Three biological replicates were done for each sample.


title: Identify LOC550643-regulated miRNAs in MDA-MB-231 cell (miRNA-Seq)

status: Public on May 26 2021

city: New Taipei

first: Kuo-Wang

last: Tsai

address: No. 289 Jianguo Road, Xindian District, New Taipei City

country: Taiwan

institute: Taipei Tzu Chi Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: The objective of this study is to unravel the metastasis-associated lncRNAs involved in the regulation of cell migration and invasion in breast cancer cells. Using next generation sequencing approach, we identify differential expression miRNAs in MDA-MB-231 cells with LOC550643 knockdown.

overall_design: Total RNA samples were derived from MDA-MB-231-IV2 cells with/without LOC550643 knockdown. Small RNA expression levels of MB-231-IV2-C and MB-231-IV2-LOC550643 knockdown were examined by using a Next-generation sequencing approach (MiSeq V2 reagent kit ).


title: Treatment of Retinoblastoma 1-Intact Hepatocellular Carcinoma With Cyclin-Dependent Kinase 4/6 Inhibitor Combination Therapy

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

summary:
Background and aims: Synthetic cyclin-dependent kinase (CDK) 4/6 inhibitors exert antitumor effects by forcing RB1 in unphosphorylated status, causing not only cell cycle arrest but also cellular senescence, apoptosis, and increased immunogenicity. These agents currently have an indication in advanced breast cancers and are in clinical trials for many other solid tumors. HCC is one of promising targets of CDK4/6 inhibitors. RB family dysfunction is often associated with the initiation of HCC; however, this is revivable, as RB family members are not frequently mutated or deleted in this malignancy.

Approach and results: Loss of all Rb family members in transformation related protein 53 (Trp53)-/- mouse liver resulted in liver tumor reminiscent of human HCC, and re-expression of RB1 sensitized these tumors to a CDK4/6 inhibitor, palbociclib. Introduction of an unphosphorylatable form of RB1 (RB7LP) into multiple liver tumor cell lines induced effects similar to palbociclib. By screening for compounds that enhance the efficacy of RB7LP, we identified an I kappa B kinase (IKK)β inhibitor Bay 11-7082. Consistently, RB7LP expression and treatment with palbociclib enhanced IKKα/β phosphorylation and NF-κB activation. Combination therapy using palbociclib with Bay 11-7082 was significantly more effective in hepatoblastoma and HCC treatment than single administration. Moreover, blockade of IKK-NF-κB or AKT pathway enhanced effects of palbociclib on RB1-intact KRAS Kirsten rat sarcoma viral oncogene homolog mutated lung and colon cancers.

Conclusions: In conclusion, CDK4/6 inhibitors have a potential to treat a wide variety of RB1-intact cancers including HCC when combined with an appropriate kinase inhibitor.

overall_design: Comparison between negative control cells and RB7LP expressed cells. There are three biological replicates for each conditions.

first: Jindan

last: Sheng

first: Susumu

last: Kohno

first: Nobuhiro

last: Okada

first: Nobuyuki

last: Okahashi

first: Fumio

last: Matsuda

first: Hiroshi

last: Shimizu

first: Paing

last: Linn

first: Naoko

last: Nagatani

first: Kana

last: Teranishi

last: Inoue

first: Seiji

last: Yano

first: Sharad

last: Kumar

first: Shunsuke

last: Kitajima

first: Itsuki

last: Ajioka

first: Chiaki

last: Takahashi


title: Identify metastasis-associated lncRNAs in MDA-MB-231 cell (microarray)

last: Tsai

type:
Expression profiling by array
Other

summary: The objective of this study is to unravel the metastasis-associated lncRNAs involved in the regulation of cell migration and invasion in breast cancer cells

overall_design: The cDNA probes derived from paired RNA samples from MDA-MB-231 cells and MDA-MB-231-IV2-1 cell. The expression levels of protein-coding gene or lncRNAs were examined by using a microarray approach (Agilent SurePrint G3 Human V2 GE)


title: Gene expression in AVPV kisspeptin cells

city: La Jolla

first: Alexander

last: Kauffman

state: California

address: 9500 Gilman Drive

department: OBGYN and Reproductive Sciences

institute: University of California San Diego

summary: Estrogen stimulates Kiss1 gene expression in AVPV cells in the brain, but whether estrogen regulates other genes in AVPV Kiss1 cells has not been determined. To provide a more detailed profiling of co-expressed genes in AVPV Kiss1 cells and determine how estrogen alters gene expression levels, we selectively isolated mRNAs from murine AVPV Kiss1 cells using transgenic-mediated immunoprecipitation and performed RNA-seq. This identified >13,000 mRNAs co-expressed in AVPV Kiss1 cells, including multiple transcripts that were positively or negatively regulated by estrogen.

overall_design: Kiss1 cells were isolated from AVPV brain punches of female mice that were estradiol (E2)-treated or ovariectomized

middle: S

first: Shannon

middle: B

last: Stephens


title: Transcriptome of hypothalamic supraoptic nucleus in response to 72h water deprivation in Wistar Han rats

status: Public on May 25 2021

city: Bristol

first: Audrys

last: Pauza

state: Somerset

address: University of Bristol, The Dorothy Hodgkin Building, Whitson Street

department: Bristol Medical School (THS)

country: United Kingdom

institute: University of Bristol

summary: The hypothalamic supraoptic nucleus (SON) is a core osmoregulatory control centre that deciphers information about the metabolic state of the organism and orchestrates appropriate homeostatic (endocrine) and allostatic (behavioural) responses. We have used RNA sequencing to describe the polyadenylated transcriptome of the SON of the male Wistar Han rat. These data have been mined to generate comprehensive catalogues of functional classes of genes (enzymes, transcription factors, endogenous peptides, G protein coupled receptors, transporters, catalytic receptors, channels and other pharmacological targets) expressed in this nucleus in the euhydrated state, and that together form the basal substrate for its physiological interactions. We have gone on to show that fluid deprivation for 3 days (dehydration) results in changes in the expression levels of 2247 RNA transcripts, which have similarly been functionally catalogued, and further mined to describe enriched gene categories and putative regulatory networks (Regulons) that may have physiological importance in SON function related plasticity.

overall_design: Transcriptomes of hypothalamic supraoptic nucleus were compared between Wistar Han rats that underwent 72h water deprivation and those that did not (control).

first: David

last: Murphy

last: Pauža

first: Michael

last: Greenwood


title: Discovery of plasma membrane associated RNAs through APEX-seq

city: Beijing

first: Xueyi

last: Teng

state: Beijing

address: No. 15 Datun road

institute: Institute of biophysics, CAS

summary: In addition to nucleic acids, a variety of biomolecules have been found on the plasma membrane. Whereas, researchers have realized that RNA has the ability to bind to membrane vesicles in vitro and connect to the plasma membrane of the cell. Hence, the combination of high-throughput sequencing and in suit labelling methods provides approaches for large-scale identification of subcellular RNAs. Here, we applied the recently published method APEX-seq, and identified 75 plasma membrane-associated RNAs, of which lncRNA PMAR72 is located around the membrane. In addition, we observed that PMAR72 was concentrated into foci in specific membrane areas. Our findings will provide some new evidence to elaborate the relationship between RNA and the plasma membrane of mammalian cells.

overall_design: APEX-seq libraries for both labeled targets and unlabeled controls were generated for the following constructs:Lck(inside), Lyn(inside), CD28(outside), PDGFR(outside).  Six to eight libraries were prepared for each construct (3 biological replicates for labeled targets, 3 biological replicates for unlabeled controls).

first: Erzhong

last: Wu

first: Xuzhen

last: Guo

first: Ruijin

last: Zhang

first: Fahui

last: Li

first: Ya

last: Cui

first: Dongdong

first: Qinghua

last: Liu

first: Jianjun

last: Luo

first: Jiangyun

last: Wang

first: Runsheng

last: Chen


title: Immune profiles of early onset vs late onset colorectal cancer

city: Portland

first: Sudarshan

last: Anand

state: OR

address: 2720 S Moody Ave

institute: Oregon Health & Science University

summary: Despite a decrease in the incidence of colorectal cancer (CRC) over the last 40 years, the incidence of CRC in people under 50 years old is increasing around the globe. Early onset (50 years old) and late onset (65 years old) CRC appear to have differences in their clinicopathological and genetic features, but it is unclear if there are differences in the tumor microenvironment. We hypothesized that the immune microenvironment of early onset CRC is distinct from late onset CRC and promotes tumor progression. We used Nanostring immune profiling to analyze mRNA expression of immune genes in FFPE surgical specimens from patients with early (N=40) and late onset (N=39) CRC. We found three genes, SAA1, C7, and CFD, have increased expression in early onset colorectal cancer and distinct immune signatures based on the tumor location. After adjusting for clinicopathological features, increased expression of CFD and SAA1 were associated with worse progression free survival and increased expression of C7 was associated with worse overall survival. We also performed gain of function experiments with CFD and SAA1 in subcutaneous tumor murine models and found that CFD is associated with higher tumor volumes, impacted several immune genes and impacted three genes in mice that were also found to be differentially expressed in early onset CRC (EGR1, PSMB9, CXCL9). Our data demonstrate that the immune microenvironment, characterized by a distinct innate immune response signature in early onset CRC, is unique, location dependent, and might contribute to worse outcomes.

overall_design: N=40 early onset and N=39 late onset CRC samples

first: Ivy

last: Gardner

first: Liana

last: Tsikitis


title: Revealing new molecular pathways for cancer cell fitness through a genetic screen of the cancer translatome

city: San Francisco

first: Duygu

last: Kuzuoglu Ozturk

address: 1450 3rd Street, Helen Diller Cancer Building

institute: UCSF

summary: The major cap binding protein eIF4E, an ancient protein required for translation of all eukaryotic genomes, is a surprising yet potent oncogenic driver. The genetic interactions that maintain the oncogenic activity of this key translation factor remain unknown. Here we carried out a genome-wide CRISPRi screen wherein we identified over 600 genetic interactions that sustain eIF4E oncogenic activity. Our data show that eIF4E controls the translation of Tfeb, a key executer of the autophagy response. This autophagy survival response is triggered by mitochondrial proteotoxic stress, which allows cancer cell survival. Our screen also reveals a functional interaction between eIF4E and a single anti-apoptotic factor, Bcl-xL, in tumor growth. Furthermore, we show that eIF4E and the exon-junction complex (EJC), involved in many steps of RNA metabolism, interact to control the migratory properties of cancer cells. Overall, we have uncovered several cancer-specific vulnerabilities that provide unprecedented resolution of the cancer translatome.

overall_design: eIF4E+/+ and eIF4E+/- MEFs expressing scramble, Magoh, eIF4A3 and Rbm8a sgRNAs were induced with Dox for 48 hours in triplicates, total RNA was isolated by Trizol and ribosomal RNA was removed by Ribo-Zero (Illumina). RNA seq libraries were prepared by ScriptSeq v2 RNA-seq library preparation kit (Epicenter) following the manufacturer’s protocol and sequenced as paired-end 100 bp on HiSeq 4000 by the Center for Advance Technology core at UCSF. RNA-seq reads were aligned to mouse GRCm38 genome by using HISAT v2.0.5 (Kim et al., 2015)with default settings. Gene read counts and expression values (measured by Transcripts Per Kilobase Million, TPM) were further calculated by RSEM v1.3.0 (Li and Dewey, 2011) with default settings. Differential expression analyses were conducted with DESeq2 (Love et al., 2014) R package, where only genes with an average TPM over 0.5 were involved.

first: Davide

last: Ruggero

first: Zhiqiang

last: Hu


title: The SNF2 ATPase-independent function of the INO80 chromatin remodeler [RNA-seq]

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: In the multi-subunit INO80 chromatin-remodeling complex, all the auxiliary subunits assemble on three distinct domains of the catalytic chromatin remodeler INO80, which are N-terminal domain, HSA domain, and ATPase domain. While the ATPase and HSA domains and the auxiliary subunits assembling on the domains are known to be responsible for ATP hydrolysis and chromatin remodeling, it is largely unknown how the auxiliary subunits assembling on the INO80 N-terminal domain regulate the chromatin status. We identify both conserved and non-conserved auxiliary subunits of the INO80 complex in Arabidopsis thaliana. All the auxiliary subunits assemble on the conserved N-terminal domain, HSA domain, and ATPase domain of INO80 in Arabidopsis. While the auxiliary subunits assembling on the INO80 ATPase domain are required for the ATPase-dependent function, the INO80 N-terminal domain and the auxiliary subunits assembling on the domain can regulate gene expression and development even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. Furthermore, we find that a subclass of the COMPASS histone H3K4 methyltransferase complexes assemble on the INO80 N-terminal domain in the INO80 complex and function together with the other auxiliary subunits assembling on the INO80 N-terminal domain, thereby facilitating the ATPase-independent function. This study suggests that the conserved chromatin remodeler INO80 has an ATPase-independent role and demonstrates that the auxiliary subunits assembling on the INO80 N-terminal domain are required for the ATPase-independent role.

overall_design: Examination of the mRNA expression of wild type, five mutants, and three transgenic lines grown under long day or short day conditions.

first: Xin

middle: J


title: Genome-wide transcriptome profiling of human Liver-Chip model of alcohol-associated liver disease (ALD) using RNA-seq.

city: Los Angeles

first: Janna

last: Nawroth

state: CA

address: 2011 Zonal Avenue

institute: USC

summary: The goal of this study was to assess RNA expression in human primary hepatocytes in response to ethanol exposure compared to control. The hepatocytes were cultured in co-culture on a Liver-Chip model with Kupffer cells and Liver sinusoidal endothelial cells (LSECs) and treated with 0.08% to 0.16% ethanol for 48h.

overall_design: Global RNA expression profiles of Liver-Chips (n=2); Liver-Chips treated with ethanol 0.08% (n=3); Liver-Chips treated with ethanol 0.16% (n=2); were generated by deep sequencing using Illumina HiSeq.

first: Dimitris

middle: V

last: Manatakis


title: MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity

city: Saint Louis

first: Ya-Lin

last: Lu

address: 660 S. Euclide Avenue

department: Developmental Biology

institute: Washington University School of Medicine

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity [Rat_Neurons_RNAseq]

summary: Neuron-enriched microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124), direct cell fate switching of human fibroblasts to neurons when ectopically expressed by repressing anti-neurogenic genes. How these miRNAs function after the onset of the transcriptome switch to a neuronal fate remains unclear. Here, we identified direct targets of miRNAs by Argonaute (AGO) HITS-CLIP as reprogramming cells activate the neuronal program and reveal the role of miR-124 that directly promotes the expression of its target genes associated with neuronal development and function.

overall_design: E18 rat cortical neurons were treated with either DMSO control or topotecan (TOPO) to reduce long gene expression. Duplicates for each condition were collected for total RNA extraction followed by RNAseq.

first: Matthew

last: McCoy

first: Andrew

last: Yoo


title: MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity [HNs_RNAseq]

overall_design: MiR-124 and ELAVL3 activities were knockdown using a tough decoy and shRNA, respectively, in primary human neurons. Duplicates for control (TuD-miR-NS + shCTL) and knockdown (TuD-miR-124 + shELAVL3) were collected for RNAseq.


title: MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity [HITS-CLIP]

overall_design: Neonatal fibroblasts were converted using miR-9/9*-124 or control, miR-NS, into neurons (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015). Cells were collected to identify transcripts with AGO-enriched binding during reprogramming. The two miR-NS and miR-9/9*-124 timepoints were processed as two biological replicates.

first: Yangjian


title: The integrated stress response is tumorigenic and constitutes a therapeutic liability in KRAS-driven lung cancer.

city: Montreal

first: Antonis

last: Koromilas

state: Quebec

address: 3755 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: 1Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital

summary: The integrated stress response (ISR) is an essential stress-support pathway increasingly recognized as a determinant of tumorigenesis. Here we demonstrate that ISR is pivotal in lung adenocarcinoma (LUAD) development, the most common histological type of lung cancer and a leading cause of cancer death worldwide. Increased phosphorylation of the translation initiation factor eIF2 (p-eIF2α), the focal point of ISR, is related to invasiveness, increased growth, and poor outcome in 928 LUAD patients. Dissection of ISR mechanisms in KRAS-driven lung tumorigenesis in mice demonstrated that p-eIF2α causes specific translational repression of dual specificity phosphatase 6 (DUSP6), resulting in increased phosphorylation of the extracellular signal-regulated kinase (p-ERK). Treatments with ISR inhibitors, including a memory-enhancing drug with limited toxicity, provides a novel therapeutic option for KRAS-driven lung cancer insofar as they substantially reduce tumor growth and prolong mouse survival. Our data provide a novel rationale for the implementation of ISR-based regimens in LUAD treatment.

overall_design: RNA seq of eIF2αS/S and eIF2αA/A KRAS G12D Tumor Cells

middle: E

first: John

last: Le Quesne

first: Ola

last: Larsson

first: Ivan

last: Topisirovic

first: Maria

last: Hatzoglou

first: Koren

middle: K

last: Mann

first: Massimo

last: Broggini

first: Helmuth

last: Popper

first: Ana

last: Teodósio

first: Leah

last: Officer

first: Nicolas

last: Ah-son

first: Urszula

last: Kazimierczak

first: Vincent

last: van Hoef

first: Cedric

last: Darini

first: Jothilatha

last: Krishnamoorthy

first: Bethany

last: Woodvine

first: Shuo

first: Nour

last: Ghaddar


title: CDH2 and Cx43 knockdown CSCs compaired with scramble (control) in breast cancer

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

summary: We report the gene expression changes in CDH2 and Cx43 knockdown CSCs as compaired to scramble (control) in MDA-MB-231

overall_design: RNA sequencing on CDH2 and Cx43 knockdown CSCs to find difference in expression from control

first: Garima

last: Sinha

first: Markos

middle: H

last: El-Far


title: Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the  delineation of DNA structure by DNA sequence

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

summary: This SuperSeries is composed of the SubSeries listed below.


title: Human Clariom D Transcriptome profiling of microRNA-mediated neuronal reprogramming with PTBP2 knockdown

first: Ya-Lin

last: Lu

summary: To identify PTBP2 targets important for neural fate acqusition, miR-9/9*-124-mediated direct conversion of human fibroblasts into neurons was employed. We showed that PTBP2 is important for the successful acquisition of neuronal fate and profiled fibroblasts and reprogrammed neurons with and without PTBP2 knockdown to identify neuronal-associated PTBP2 targets during reprogramming.

overall_design: Human Clariom D array profiling of 3 sets of samples each with duplicates at day 14 with miR-NS, miR-9/9*-124 shCTL and miR-9/9*-124 shPTBP2

first: Andrew

last: Yoo


title: Genetic compensation for cilia defects in cep290/NPHP6 mutants by upregulation of cilia-associated small GTPases

city: Bar Harbor

first: Iain

middle: A

last: Drummond

state: Maine

address: 159 Old Bar Harbor Road Bar Harbor

department: Davis Center for Regenerative Biology and Aging

institute: Mount Desert Island Biological Laboratory

summary: Mutations in CEP290, a large multidomain coiled coil protein, are associated with multiple cilia-associated syndromes. Over 130 CEP290 mutations have been linked to a wide spectrum of human ciliopathies, raising the question of how mutations in a single gene cause different disease syndromes. In zebrafish the expressivity of cep290 deficiencies were linked to the type of genetic ablation: acute cep290 morpholino knockdown caused severe cilia-related phenotypes while defects in a Crispr/Cas9 genetic mutant were restricted to photoreceptor defects. Here we show that milder phenotypes in genetic mutants were associated with upregulation of genes encoding the cilia-associated small GTPases arl3, arl13b, and unc119b. Upregulation of UNC119b was also observed in urine-derived renal epithelial cells from human JBTS CEP290 patients. Ectopic expression of arl3, arl13b and unc119b in cep290 morphant zebrafish embryos rescued Kupffer's vesicle cilia and partially rescued photoreceptor outer segment defects. The results suggest that genetic compensation by upregulation of genes involved in a common subcellular process, lipidated protein trafficking to cilia, may be a conserved mechanism contributing to genotype-phenotype variations observed in CEP290 deficiencies.

overall_design: RNA from 72hpf zebrafish embryos was analyzed. Each sample consisted of pools of 30 embryos from cep290 morphants, maternal zygotic mutants or wildtype embryos. Biological triplicates were done.

first: Magdalena

last: Cardenas-Rodriguez

first: Christina

last: Austin-Tse

first: Judith

last: Bergboer

first: Elisa

last: Molinari

first: Yuya

last: Sugano

first: Ruxandra

last: Bachmann-Gagescu

first: John

last: Sayer


title: DNA methylation patterns in juvenile systemic sclerosis and localized scleroderma

status: Public on May 24 2021

city: Pittsburgh

first: Amr

last: Sawalha

address: 4401 Penn Avenue

institute: University of Pittsburgh

type: Methylation profiling by genome tiling array

summary: Scleroderma refers to a group of chronic fibrotic immune-mediated diseases of unknown etiology. Characterizing epigenetic changes in childhood-onset scleroderma, systemic sclerosis or localized scleroderma, has not been previously performed. The aim of this study was to assess DNA methylation differences and similarities between juvenile systemic sclerosis (jSSc) and juvenile localized scleroderma (jLS) compared to matched healthy controls. Genome-wide DNA methylation changes in peripheral blood mononuclear cell samples were assessed using the MethylationEPIC array followed by bioinformatic analysis and limited functional assessment. We identified a total of 105 and 144 differentially methylated sites compared to healthy controls in jSSc and jLS, respectively. The majority of differentially methylated sites and genes represented were unique to either jSSc or jLS suggesting a different underlying epigenetic pattern in both diseases. Among shared differentially methylated genes, methylation levels in a CpG site in FGFR2 can distinguish between LS and healthy PBMCs with a high accuracy. Canonical pathway analysis revealed that inflammatory pathways were enriched in genes differentially methylated in jSSc, including STAT3, NF-κB, and IL-15 pathways. In contrast, the HIPPO signaling pathway was enriched in jLS. Our data also suggest a potential role for NOTCH3 in both jSSc and jLS, and revealed a number of transcription factors unique to each of the two diseases. In summary, our data revealed important insights into jSSc and jLS and suggest a potentially novel epigenetic diagnostic biomarker for LS.

overall_design: The study cohort consisted of DNA methylation profiles of PBMCs isolated from peripheral blood of forty-eight juvenile systemic sclerosis and localized scleroderma patients and healthy pediatric controls recruited from the National Registry for Childhood Onset Scleroderma. Participants were grouped into 16 triads by matching for age (within five years), sex, and self-reported ancestral background.

first: Patrick

last: Coit


title: Bisection of the X Chromosome Disrupts the Initiation of Chromosome Silencing during Meiosis in Caenorhabditis elegans

city: Jerusalem

first: Yonatan

last: Tzur

address: Givat-Ram

country: Israel

institute: Hebrew University of Jerusalem

summary: During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments were enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome were upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.

overall_design: CRISPR mediated bisection of the X chromosoeme in C. elegans to create YBT7 strain. Comparative transcriptomics of YBT74 to WT

first: Yisrael

last: Rappaport

first: Hanna

last: Achache

first: Roni

last: Falk

first: Omer

last: Murik

first: Oren

last: Ram


title: RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after Twist1 knockout in mouse bone marrow stromal cells

city: TianJin

first: Xiao Tong

last: Ma

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

summary:
Purpose: The goals of this study are to determine possible  downstream targets of Twist1  in bone marrow stromal cells  with or without Twist1 knockout.
Methods: gene expression profiling with or without Twist1 knockout in bone marrow stromal cells  were generated by deep sequencing, using Illumina Hiseq.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays.
Conclusions: Notch signaling were activated after Twist1 knockout.

overall_design: mRNA profiles of stromal cells   with or without Twist1 knockout were generated by deep sequencing using Illumina Hiseq.

first: Xiaotong

first: Xiaoyan

last: Liu


title: Sex-specific differences in the function and differentiation of ABCs contribute to the female bias in lupus pathogenesis

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: We report the application of RNA-seq, ATAC-seq, and CUT and RUN technology for high-throughput profiling of H3K27me3 epigenetic marks in mice SWAP-70 and DEF6 double knockout (DKO) B-lymphocytes (ABCs and FoBs) flow sorted from spleen.   We show that ABCs from female and male DKO mice have unique transcriptional profiles, chromatin accessibility, and that there is a selective loss of repressive chromatin marks like H3K27me3 in ABCs of DKO females can contribute to the increased expression of X-chromosome linked genes like Tlr7 and several other loci among which Tbx21, the classical ABC marker, showed strongest loss in F-ABCs as compared to F-FoBs.

overall_design:
RNAseq: 16 RNAseq samples with 2-4 replicas separated between two experiment
ATACseq: 3 ATACseq samples with 2 replicas each
Cut and Run: 8 samples with 3 replicas each

first: Edd

last: Ricker

first: Michela

last: Manni

first: Danny

last: Flores-Castro

first: Daniel

last: Jenkins

first: Sanjay

last: Gupta

first: Juan

last: Rivera-Correa

first: Wenzhao

last: Meng

first: Aaron

middle: M

last: Rosenfeld

first: Tania

last: Pannellini

first: Mahesh

last: Bachu

first: Peter

last: Sculco

first: Rolf

last: Jessberger

first: Eline

middle: T

last: Luning Prak

first: Alessandra

last: Pernis


title: A computational framework for identifying promoter sequences in non-model organisms using RNA-seq datasets

city: Seattle

first: Erin

last: Wilson

state: WA

address: 185 E Stevens Way NE

department: The Paul G. Allen School of Computer Science & Engineering

institute: University of Washington

summary: We developed a computational framework to discover short DNA sequences that confer strong expression in non-model organisms. The framework relies solely on whole genome and RNA sequencing data types, which are easily accessible to a variety of research groups. The framework proceeds in three main stages: 1) identification of a group of highly expressed loci that maintain high transcript counts across a broad range of experimental conditions, 2) extraction of the corresponding upstream candidate promoter regions of these highly expressed loci while minding nearby annotations and avoiding those that may potentially reside in operons, and 3) application of the motif finding algorithm in BioProspector to these upstream regions to predict the location and sequence of the -35 and -10 hexamers that drive the strong expression of these loci. Ultimately, we report sequences of 27-30 bases in length as candidate -35, -10 signals for each of the top loci and create a consensus motif from these predictions. We apply our framework to 80 RNA-seq datasets collected for the methanotroph Methylotuvimicrobium buryatense 5GB1 and validate our predictions computationally and experimentally. The data deposited here represent all RNA-seq data that, until this study, has not previously been published.

overall_design: 80 RNA-seq datasets measuring Methylotuvimicrobium buryatense expression across 12 experimental growth conditions were compiled from a previously published data sets, additionally including their associated quality control runs, and several previously unpublished experiments. RNA-seq data were generated from a mix of Illumina protocols using a variety of read lengths (36, 50, and 150 bp) and paired and unpaired libraries. Of these 80 datasets, 24 have been previuosly published and deposited. The remaining 56 samples are deposited here.

first: David

last: Beck

first: Joseph

last: Groom

first: M

last: Sarfatis

first: Stephanie

last: Ford

first: Mary

last: Lidstrom


title: Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition [ChIP-seq]

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

institute: Oregon Health and Science University

summary: Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. A near universal feature of centromeres is the presence of repetitive sequences, such as satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. Previously, we identified a novel composite retrotransposon, LAVA, that is exclusive to gibbons and expanded within the centromere regions of one gibbon genus, Hoolock. In this study, we use ChIP-seq, RNA-seq and fluorescence in situ hybridization to comprehensively investigate the repeat content of centromeres of the four extant gibbon genera (Hoolock, Hylobates, Nomascus and Siamang). We find that CENP-A nucleosomes and the DNA-protein interface with the inner kinetochore are enriched in retroelements in all gibbon genera, rather than satellite DNA. We find that LAVA in Hoolock is enriched in the centromeres of most chromosomes and shows centromere- and species-specific sequence and structural differences compared to other genera, potentially as a result of its co-option to a centromeric function. In contrast, we found that a centromeric retroelement-derived macrosatellite, SST1, corresponds with chromosome breakpoint reuse across gibbons and shows high sequence conservation across genera. Finally, using de novo assembly of centromere-specific sequences, we determine that transcripts originating from gibbon centromeres recapitulate species-specific TE diversity. Combined, our data reveals dynamic, species-specific shifts in repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity observed within this lineage.

sample_organism:
Symphalangus syndactylus
Nomascus leucogenys
Hylobates moloch
Hoolock leuconedys

overall_design: ChIP-seq against three centromere proteins (CENP-A, CENP-B and CENP-C) was carried out on four gibbon species, representing the four extant gibbon genera (Siamang, Hylobates, Hoolock and Nomascus).

first: Gabrielle

last: Hartley

first: Rachel

last: O'Neill

first: Lucia

last: Carbone


title: MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity [TD_RNAseq]

first: Ya-Lin

last: Lu

overall_design: Adult dermal fibroblasts were converted using miR-9/9*-124 into neurons (Yoo et al., 2011; Richner et al., 2015; Abernathy et al., 2017). To examine the importance of miR-124, miR-124 activity was knockdown using either tough decoy control, TuD-miR-NS, or tough decoy against miR-124, TuD-miR-124. Triplicates for each condition was collect at day 21 and total RNA was collect for RNAseq.

first: Andrew

last: Yoo


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR487KVV)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
H3K4me1 ChIP-seq on primary keratinocytes in day 0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: An Engineered IL-15 Cytokine Mutein Fused to an Anti-PD1 Antibody Improves Intratumoral T Cell Function and Anti-tumor Immunity (human)

city: Rotterdam

last: Campos Carrascosa

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary:
Background: Cancer Immunotherapy with cytokines has demonstrated clinical efficacy but is frequently accompanied with severe adverse events caused by excessive and systemic immune activation. Here, we addressed these challenges by engineering a fusion protein of a single, potency-reduced, IL-15 mutein and an anti-PD1 antibody (αPD1-IL15m). This immunocytokine is designed to deliver PD1-mediated avidity-driven IL-2/15 receptor stimulation preferentially to PD1-positive tumor-infiltrating lymphocytes (TILs) while reducing the natural preference of IL-15 for circulating peripheral NK or T cell
Methods: We isolated human lymphocytes from resected hepatocellular carcinoma tissue and cultured these tumor-infiltrating lymphocytes (TILs) in vitro in the presence or absence of an PD1-targeted IL15 mutein, anti-PD1 antibody or IL-15 agonist. After 9 days, CD4+ TILs and CD8+ TILs were sorted by FACS and RNA of 3,000 to 150,000 cells was isolated.
Results: The PD1-IL15 fusion cytokine enhanced pro-survival, proliferation and activation pathways in tumor-infiltrating CD4+ and CD8+ cells compared to untreated controls as well as to the combined treatment of single agents (anti-PD1 antibody and IL-15 agonist)

overall_design: RNA-Seq of HCC-derived TILs after 9 days in vitro in the absence (ctrl) or presence of PD1-IL15 (m2) or the combined treatment of anti-PD1 and IL-15 agonist (comb).

first: Jaap

last: Kwekkeboom

first: Keith

last: Ching

first: Wenjing

last: Yang

first: Tim

last: Fisher


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR392EMS)

summary:
H3K4me1 ChIP-seq on primary keratinocytes in day 3 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR793NQA)

summary:
H3K27me3 ChIP-seq on primary keratinocytes in day 3 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the  delineation of DNA structure by DNA sequence (SS-Seq)

first: Barbara

last: Meyer

summary: We developed an efficient method to map DNA supercoils that quantifies genome-wide incorporation of biotinylated psoralen using high throughput DNA sequencing and applied it to C. elegans. We discovered that GC-rich regions flanked by sharp GC/AT boundaries delineate the extent of negative supercoiling at transcription start sites, the regions of DNA accessibility and the positioning of nucleosomes.  We also discovered that promoters with either paused or non-paused RNA polymerase II (Pol II) exhibit the same level of supercoiling, revealing that supercoiling at transcription start sites is neither the cause nor consequence of Pol II pausing.  Furthermore, we found that a condensin complex that mediates X-chromosome dosage compensation in C. elegans creates local negative supercoils at its high-occupancy binding sites on X but does not create large domains of supercoiling across X to achieve dosage compensation.  We also developed a new high-throughput method to map single-stranded DNA and alternative DNA structures, including Z DNA. The approach combines potassium permanganate footprinting and a technique to sequence rare double-stranded breaks.  We discovered that GC-rich regions flanked by sharp GC/AT boundaries determine the width of single-stranded DNA regions at transcription start sites.  Moreover, AT-rich sequences bordered by a change in GC content delineate Z DNA at transcription end sites and in introns as well as non-B DNA at trans-splicing acceptor sites that comprise the 5' ends of most mature mRNAs in C. elegans.  Our analysis suggests that a sharp transition in GC content rather than the GC content by itself creates alternative DNA structures.

overall_design: We performed potassium permanganate footprinting in C. elegans wild type and dosage compensation defective embryos, starved first stage larvae and larvae treated with a-amanitin to inhibit transcription.

first: Kristina

last: Krassovsky


title: Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the  delineation of DNA structure by DNA sequence (BP-Seq)

overall_design: We performed mapping of supercoils using biotinylated psoralen in wt embryos, starved first stage larvae, dosage compensation mutant embryos and first stage larvae treated with a-amanitin to inhibit transcription.


title: Multiplexed protein and drug imaging by super-resolution ion beam imaging

city: Boston

first: Sizun

last: Jiang

state: MA

address: 3 Blackfan Circle

institute: BIDMC/Harvard

summary: Simultaneous visualization of the relationship between multiple biomolecules and their ligands or small molecules at the nanometer scale in cells will enable greater understanding of how biological processes operate. We present here high-definition multiplex ion beam imaging (HD-MIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added structurally-unmodified small molecules. With this technology, the atomic constituents of the biomolecules themselves can be used in our system as the “tag” and we demonstrate measurements down to ~30 nm lateral resolution. We correlated the subcellular localization of the chemotherapy drug cisplatin simultaneously with five subnuclear structures. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. Unexpectedly, cells surviving multi-drug treatment with cisplatin and the BET inhibitor JQ1 demonstrated near total cisplatin exclusion from the nucleus, suggesting that selective subcellular drug relocalization may modulate resistance to this important chemotherapeutic treatment. Multiplexed high-resolution imaging techniques, such as HD-MIBI, will enable studies of biomolecules and drug distributions in biologically relevant subcellular microenvironments by visualizing the processes themselves in concert, rather than inferring mechanism through surrogate analyses.

overall_design: Paired-end RNAseq of cisplatin-treated cells.

first: Bokai

last: Zhu

first: Xavier

last: Rovira-Clave

first: Garry

last: Nolan


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR621FNM)

summary:
H3K27me3 ChIP-seq on primary keratinocytes in day 0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR637ISS)

summary:
H3K27ac ChIP-seq on primary keratinocytes in day 6 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Time-course RNA-seq analysis of salt resonse in Arabidopsis and Marchantia

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

summary: Purpose: To understand the dynamic salt-sress response in Arabidopsis and Marchantia

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana
Oryza sativa Japonica Group

overall_design: 7-day old Arabidopiss seedlings , rice seedlings and Marchantia gemmalings were subjected to  100 mM NaCl  for 0, 1, 2, 3, 6, 12, 24,48 and 72 hr, 2-3  biological replicates

first: Ting-Ying

last: Wu


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR709ABP)

summary:
H3K27ac ChIP-seq on primary keratinocytes in day 3 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Weight Loss after Roux-En Y Gastric Bypass Surgery Reveals Novel Skeletal Muscle Promoter-Specific DNA Methylation Changes in Obese Patients

city: Tucson

first: Dawn

last: Coletta

state: AZ

address: 1501 N. Campbell Ave

institute: UNIVERSITY OF ARIZONA

type: Methylation profiling by high throughput sequencing

summary: The mechanisms of weight loss and metabolic improvements following bariatric surgery in skeletal muscle are not well known, however epigenetic modifications are likely to contribute. The aim of our study was to investigate skeletal muscle DNA methylation after weight loss induced by Roux-en-Y gastric bypass (RYGB) surgery.

overall_design: Muscle biopsies were obtained basally from seven insulin-resistant obese (BMI >40 kg/m2) female subjects (45.1±3.6 years) pre and 3 months post-surgery with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. Four lean (BMI <25 kg/m2) females (38.5±5.8 years) served as controls. We performed reduced representation bisulfite sequencing next generation methylation on DNA isolated from the vastus lateralis muscle biopsies.

first: Richard

middle: L

first: Luis

last: Garcia


title: Ex vivo scRNA-Seq of CD4+ cells in T-bet deficiency and wild type

status: Public on May 22 2021

city: Bellinzona

first: Mathilde

last: Foglierini

address: Via Vincenzo Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

summary: Starting from frozen PBMCs of a patient with T-bet deficiency and a wild type control, CD4+ cells were enriched by magnetic sorting. The cells were either activated with plate-bound anti-CD3/anti-CD28 monoclonal antibodies for 14 hours or left untreated. Single-cell RNA sequencing (scRNA-Seq) was performed to study differentially expressed genes in the T helper cell compartment in T-bet deficiency.

overall_design: Ex vivo scRNA-Seq analysis of CD4+ enriched cells from a patient with T-bet deficiency and wild type control

first: Federica

last: Sallusto

first: Marc

last: Weisshaar

first: Samuele

last: Notarbartolo

first: Andrea

last: Rinaldi

first: Ivo

last: Kwee

first: Murodzhon

last: Akhmedov


title: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes [RNA-seq]

city: Oxford

first: Thomas

last: Milne

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

institute: University of Oxford

summary: Regulatory interactions mediated by transcription factors (TFs) make up complex networks that control cellular behavior. Fully understanding these gene regulatory networks (GRNs) offers greater insight into the consequences of disease-causing perturbations than can be achieved by studying single TF binding events in isolation. Chromosomal translocations of the lysine methyltransferase 2A (KMT2A) produce KMT2A fusion proteins such as KMT2A-AFF1 (also known as MLL-AF4), causing poor prognosis acute lymphoblastic leukemias (ALLs) that sometimes relapse as acute myeloid leukemias (AMLs). KMT2A-AFF1 is thought to drive leukemogenesis through direct binding and inducing aberrant overexpression of key gene targets, such as the anti-apoptotic factor BCL2 and the proto-oncogene MYC. However, studying direct binding alone doesn’t allow for network generated regulatory outputs, including the indirect induction of gene repression. To better understand the KMT2A-AFF1 driven regulatory landscape, we integrated ChIP-seq, patient RNA-seq and CRISPR essentiality screens to generate a model GRN. This GRN identified several key transcription factors, including RUNX1, that regulate target genes downstream of KMT2A-AFF1 using feed-forward loop (FFL) and cascade motifs. A core set of nodes are present in both ALL and AML, and CRISPR screening revealed several factors that help mediate response to the drug venetoclax. Using our GRN, we then identified an KMT2A-AFF1:RUNX1 cascade that represses CASP9, as well as KMT2A-AFF1 driven FFLs that regulate BCL2 and MYC through combinatorial TF activity. This illustrates how our GRN can be used to better connect KMT2A-AFF1 behavior to downstream pathways that contribute to leukemogenesis, and potentially predict shifts in gene expression that mediate drug response.

overall_design: Nascent RNA-seq on SEM or RS4;11 cell lines treated with RUNX1 siRNA, MLL-AF4 siRNA or non-targeting control. N=3 / biological group.

first: Joe

middle: R

last: Harman

first: Ross

last: Thorne

first: Max

last: Jamilly

first: Nicholas

last: Crump


title: Circulating exosomal miRNA signature in pregnancies with gestational diabetes mellitus across gestation

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

institute: University of Queensland

summary: The aim of this study was to establish the exosomal miRNA profile across gestation in normal and GDM pregnancies and to determine the signaling pathways associated with the changes in the miRNA profile in GDM.

overall_design: miRNAs were profiled from exosomes using next generation seqeuencing (Illumina NextSeq 500 platform).

first: Soumyalekshmi

last: Nair

first: Carlos

last: Salomon


title: Genome-wide maps of histone modifications in CX3CR1+ effector , CX3CR1- Ly108- exhausted, or Ly108+  progenitor CD8 T cells during chronic viral infection.

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary: During chronic viral infection, pathogen-specifc CD8+ T cells develop into three main phenotypically and functionally distinct subsets:  TCF1hi progenitor,  PD-1hi exhausted, and recently identied CX3CR1+ cytotoxic effector cells. Although genetic programs governing progenitor and exhausted subset formation have been well-studied, how CX3CR1+ effector CD8+ T cell differentiation is transcriptionally and epigentically regulated remains elusive. In this study, our single cell transcriptomics and epigenetic assays revealed that three subsets of virus-specific cells were governed by distinct gene regulatory networks (GRNs) and epigenetic landscapes. Computational analyses demonstrated a striking similarity between the CX3CR1+ subset and short-live effector cells (SLECs) from acute LCMV infection. Consistently, genetic deletion of  T-bet (Tbx21) significantly diminished the formation and function of the CX3CR1+ subset. Importantly, we identify that the transcription factor (TF) BATF is required to maintain a permissive chromatin structure that allows differentiation transition from TCF1+ progenitor to CX3CR1+ effector cells. Intriguingly,  haplodificiency of BATF in CD8+ T cells abolished CX3CR1+ effector subset formation. Lastly, we found that BATF directly bound to key genetic regions such as Tbx21 and modulated their enhancer accessibility to facilitate progenitor to CX3CR1+ effector cell transition. These mechanistic insights can be harnessed to overcome T cell exhaustion in treating chronic infections and cancer.

overall_design: H3K4me3, H3K27ac, and H3K27me3 CUT&TAG ChIPseq, 3 samples (CX3CR1+ , CX3CR1- Ly108- PD1+, or Ly108+  CD8 T cells), 2 biological replicates per sample, from LCMV-Cl13 infected C57BL/6 mice.

first: Yao

last: Chen


title: Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [scRNA-Seq]

city: Tokyo

first: Sanshiro

last: Kanazawa

address: 7-3-1, Hongo, Bunkyo-ku

department: Oral and Maxillofacial Surgery

institute: The University of Tokyo Hospital

summary: Although multiple studies have investigated the mesenchymal stem and progenitor cells (MSCs) that give rise to mature bone marrow, high heterogeneity in their morphologies and properties causes difficulties in molecular separation of their distinct populations. In this study, by taking advantage of the resolution of the single cell transcriptome, we analyzed Sca-1 and PDGFR-α fraction in the mouse bone marrow tissue. The single cell transcriptome enabled us to further classify the population into seven populations according to their gene expression profiles. We then separately obtained the seven populations based on candidate marker genes, and specified their gene expression properties and epigenetic landscape by ATAC-seq. Our findings will enable to elucidate the stem cell niche signal in the bone marrow microenvironment, reconstitute bone marrow in vitro, and shed light on the potentially important role of identified subpopulation in various clinical applications to the treatment of bone- and bone marrow-related diseases.

overall_design: Identification of subpopulations in mouse bone marrow MSCs by single-cell level

first: Kazuto

last: Hoshi


title: Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [ATAC-Seq]


title: Chromatin accessibility landscapes of CX3CR1+ effector , CX3CR1- Ly108- exhausted, or Ly108+  progenitor CD8 T cells during chronic viral infection.

department: Pathology

overall_design: ATACseq, 3 samples (CX3CR1+ , CX3CR1- Ly108- , or Ly108+  CD8 T cells), 2 biological replicates per sample, from LCMV-Cl13 infected C57BL/6 mice.


title: Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [RNA-Seq]


title: RNA-sequence analysis of mouse AAA samples obtained from ApoE-/- and ApoE-/-Nur77-/-  mice induced by Ang II

status: Public on May 21 2021

city: Shanghai

first: hengyuan

last: zhang

address: 160 Pu Jian Road

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: We report the transcriptomic analysis of RNA-seq of abdominal aortas isolated from ApoE-/- and ApoE-/-Nur77-/- mice mice exposed to Ang II to uncover the mechanisms underlying the undefined role of Nur77 in abdominal aortic aneurysm (AAA)

overall_design: Comparison of mouse abdominal aortic samples obtained from ApoE-/- and ApoE-/-Nur77-/- mice perfused with Ang II

first: Hengyuan

last: Zhang

first: Qin

last: Shao


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR736ZEG)

first: ENCODE

last: DCC

summary:
H3K27ac ChIP-seq on primary keratinocytes in day 0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR243ZGI)

summary:
H3K4me1 ChIP-seq on primary keratinocytes in day 6 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Bulk RNAseq of Aire-Expressing Cells from Pregnant vs Virgin Mice

city: San Francisco

first: Tippi

last: MacKenzie

address: 550 16th Street

department: Surgery, Pediatrics, Center for Maternal-Fetal Precision Medicine

institute: University of California, San Francisco

summary: We had previously found that ablating autoimmune regulator (Aire)-expressing cells during pregnancy lead to fetal loss, intruterine growth restriction, and the specific expansion of Tfh populations. To investigate transcriptional changes in Aire+ cells, specifically in medullary thymic epithelial cells (mTECs) and extrathymic Aire-expressing cells (eTACs), we used the Aire-Driven Igrp-GFP (Adig) reporter mouse. We sorted mTECs and eTACs from virgin Adig females and E9.5 pregnant Adig dams for bulk RNA sequencing. While we found no differences in the frequency or absolute number of mTECs or eTACs, or of Aire expression in mTECs or eTACs during pregnancy, we did find a significant number of differentially expressed (DE) transcripts during pregnancy in splenic eTACs, and almost no changes in mTECs. Pathway analysis of splenic DE genes revealed enrichment for erythrocyte development and included a number of putative PAAs such as embryonic hemoglobin theta. While these transcriptional changes may represent eTAC-intrinsic expression of PAAs, pregnancy also causes increased maternal hematopoiesis as well as passage of fetal nucleated RBCs into the maternal circulation and the immunologic relevance of this phenomenon requires further study.

overall_design: Seven Adig females were bred to BALB/c males and sacrificed on day 9 of pregnancy, and six age-matched virgin females were sacrified on the same day. Stromal cells were prepared for cell sorting by mincing thymus, lymph nodes, and spleen with razor blades and sujected to a Percoll gradient. Isolated cells from these tissues were stained for CD3, CD19, NK1.1, MHCII, and live/dead marker. CD3- CD19- NK1.1- MHCII+ GFP+ cells were sorted via FACS, resuspended in lysis bffer, and snap frozen for RNA isolation and sequencing.  We employed standard mRNA-seq protocols used by the UCSF Functional Genomics sequencing core. 52 samples were spread across 8 conditions, each with 6-7 replicates.  49 samples are represented in this dataset.

first: Eva-Gillis

last: Buck

first: Marina

last: Sirota


title: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes [CRISPR sgRNA screen]

first: Thomas

last: Milne

overall_design: CRISPR sgRNA dropout/enrichment screen using the TKOv3 sgRNA library in THP1 cells with 18 days Venetoclax treatment and no treatment controls. N=2 / biological group.

first: Joe

last: Harman

first: Ross

last: Thorne


title: Histone ChIP-seq from foreskin keratinocyte (ENCSR812GLE)

summary:
H3K27me3 ChIP-seq on primary keratinocytes in day 6 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes [ChIP-seq]

overall_design: ChIP-seq profiling of SEM, RS4;11 and THP1 cell lines, and patient ALL blasts. Antibodies used against MAZ, RUNX1, MLL-N and AF4-C. Reference normalised ChIP-seq performed with SEM cells following RUNX1/non-targeting siRNA treatment.

first: Max

last: Jamilly

first: Nicholas

last: Crump


title: Genome-wide DNA Methylation Analysis along the Progression of Gastric Marginal Zone B-cell Lymphoma of MALT Type

city: Ulm

middle: FE

last: Barth

state: Select...

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University

summary: Extranodal marginal zone B-cell lymphoma (MZBL) of the mucosa-associated lymphoid tissue (MALT) is an indolent lymphoma mostly affecting the gastrointestinal tract. In the stomach, MZBL of MALT initially has small cell morphology (SC-MZBL) and arises in the background of Helicobacter pylori induced gastritis. Clonal malignant progression to large cell morphology (LC-MZBL) is observed. During this progression an intermediate stage consisting of both the small cell and large cell morphology is present, called "composite lymphoma". To gain insight into the DNA methylation changes associated with progression of gastric MZBL of MALT, we performed genome-wide DNA methylation profiling using the Illumina Infinium MethylationEPIC BeadChip array  for 30 microdissected samples of gastric MZBL of MALT.

overall_design: Bisulphite converted DNA from 30 gastric MZBL of MALT samples were amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip.

first: Rucha

last: Dugge

first: Rabea

last: Wagener

first: Peter

last: Mӧller

middle: F


title: Chromatin assembly factor 1B critically controls early development but not functional acquisition of iNKT cells [RNA-seq]

first: Yu

last: Xu

address: 320 Yueyang Road

institute: Shanghai Institue of Biochemistry and Cell Biology

summary: T cell development is a complicatedly hierarchical process which is closely related with the chromatin activation and gene transcription. CD4+CD8+ double-positive (DP) thymocytes give rise to both conventional TCRαβ+ T cells and natural killer T cells, but they display different characteristics. Compared with conventional TCRαβ+ T cells, invariant natural killer T cells (iNKT cells) as the major population of NKT cells, are CD1d-restricted, recognize glycolipid antigens and rapidly exert effector functions after stimulation. However, the specific molecular mechanism of early iNKT cell development remain incompletely understood. Here the authors show that deletion of Chromatin assembly factor 1B (CHAF1b) remains the normal development of conventional TCRαβ+ T cell, but specifically impacts iNKT cell generation and completely impairs iNKT cell development from stage 0 with a PLZF independent way. This dysregulation is accompanied by a specific decrease in gene transcription of Vα14-Jα18, an impairment in TCR signaling and PLZF expression. Notably, ectopic expression of a transgenic Vα14-Jα18 TCR completely rescues these defects in Chaf1b-deficient iNKT cells. Moreover, cytokine secretion and anti-tumor activity are substantially maintained in Chaf1b-deficient iNKT cells with transgenic Vα14-Jα18 TCR. Our study identifies CHAF1b as a distinct regulator controls early development of iNKT cells via transcriptional regulation of Vα14-Jα18.

overall_design: DP thymocytes of wild type (WT) and Chaf1b-deficient (KO) mice were analyzed gene expression by RNA-seq with two replications.

first: Junwei

last: Ma

first: Haorui

last: Luo

first: Yaohuang

last: Shi

first: Haifeng

last: Liu

first: Ao

last: Sun

first: Xiaolong


title: Chromatin assembly factor 1B critically controls early development but not functional acquisition of iNKT cells


title: Comparisons of Nasal Polyp ASC, Nasal polyp IgD+ (naïve-like) B cells, and Blood naïve B cells

status: Public on May 20 2021

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: Here we investigate the transcriptional landscapes of nasal polyp IgD+ (naïve-like) B cells, nasal polyp ASC, and blood naïve B cells using RNA-seq.  These data found that nasal polypP IgD+ naïve-like B cells are activated and similar to nasal polyp ASC and distinct from circulating B cells in the blood.

overall_design: Bulk RNA-seq of FACS sorted B cells and ASC from the nasal polyp tissues compared to blood naïve  B cells.

first: Christohper

middle: D


title: Elevated HIV trans-infection of CD4 T cells in MRKAd5 vaccine recipients due to CD8 T cells targeting of adapted epitopes

city: Birmingham

first: Kai

last: Qin

state: Alabama

address: Microbiology/845 19th Street South

department: Department of Medicine

institute: University of Alabama at Birmingham

summary: We report the application of single-cell-based RNA sequencing technology for high-throughput profiling of antigen specific CD8 T cells induced by MRKAd5 vaccine (HVTN502 trial). Based on the transcriptomic data, we identified 68 differentially expressed genes comparing adapted versus non-adapted epitope specific CD8 T cells. Interestingly, CLOCK and HNF1B, which are critical for circadian rhythm, were found to be upregulated in both recipients with the non-adapted epitope specific CD8 T cell responses.

overall_design: The mRNA profiles of MRKAd5 vaccine-encoded non-adapted and adapted epitope specific CD8 T cell after in vitro expansion using autologous peptide pulsed monocytes were examined.


title: The Rhox gene cluster suppresses germline LINE1 transposition

city: La Jolla

first: Kun

last: Tan

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

summary: Transposable elements (TEs) are mobile sequences that engender widespread mutations and thus are a major hazard that must be silenced. The most abundant active class of TEs in mammalian genomes is long interspersed element class 1 (LINE1).  Here, we report that LINE1 transposition is suppressed in the male germline by transcription factors encoded by a rapidly evolving X-linked homeobox gene cluster. LINE1 transposition is repressed by many members of this RHOX transcription factor family, including those with different patterns of expression during spermatogenesis. One family member—RHOX10—suppresses LINE1 transposition during fetal development in vivo when the germline would otherwise be susceptible to LINE1 activation because of epigenetic reprogramming. We provide evidence that RHOX10 suppresses LINE transposition by inducing Piwil2, which encodes a key component in the Piwi-interacting (pi) RNA pathway that protects against TEs. The ability of RHOX transcription factors to suppress LINE1 is conserved in humans, but is lost in RHOXF2 mutants from several infertile human patients, raising the possibility that loss of RHOXF2 causes human infertility by allowing uncontrolled LINE1 expression in the germline. Together, our results support a model in which the Rhox gene cluster is in an evolutionary arms race with TEs, resulting in expansion of the Rhox gene cluster to suppress TEs in different biological contexts.

overall_design: FACS-purified germ cells from fetal Rhox10-null;Oct4-eGFP+/+ (KO) and littermate Oct4-eGFP+/+ (control) mice were used for RNA-seq.

first: Miles

last: Wilkinson


title: Cardiac organoids reveal mechanisms of human cardiogenesis

city: Vienna

first: Pablo

last: Hofbauer

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

summary: Self-organisation and coordinated morphogenesis of multiple cardiac lineages is essential for the development and function of the heart. However, the absence of a human in vitro model that mimics the basic lineage architecture of the heart hinders research into developmental mechanisms and congenital defects. Here, we describe the establishment of a reliable, lineage-controlled and high-throughput cardiac organoid platform. We show that cardiac mesoderm derived from human pluripotent stem cells robustly self-organises and differentiates into cardiomyocytes forming a cavity. Co-differentiation of cardiomyocytes and endothelial cells from cardiac mesoderm within these structures is required to form a separate endothelial layer. As in vivo, the epicardium engulfs these cardiac organoids, migrates into the cardiomyocyte layer and differentiates. Thus, the cardiac organoid platform represents a powerful resource for the quantitative and mechanistic analysis of early human cardiogenesis that is otherwise inaccessible.

overall_design: Human pluripotent stem cells were differentiated into 2D cardiomyocytes, 2D endothelial cells, 3D assembled CM structures, 2D and 3D epicardial cells and 3D cardiac organoids consisting of 1) mainly cardiomyocytes or 2) cardiomyocytes and endothelial cells. 2D Human cardiac microvascular endothelial cells were used as a control endothelial cell population.

first: Stefan

last: Jahnel

first: Nora

last: Papai

first: Sasha

last: Mendjan


title: Expression profiling of microRNA from peripheral blood of dairy cows in response to Staphylococcus aureus-infected mastitis

city: Yinchuan

first: Xing-Ping

last: Wang

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

institute: Ningxia University

summary:
Purpose: To identify the expression profiling of miRNA in peripheral blood of dairy cows in response to S. aureus-infected mastitis and explore the biomarkers for early diagnosis of S. aureus-infected mastitis.  Methods: RNAseq technology was used to determine the expression profiles of microRNA (miRNA) from peripheral blood of Chinese Holstein cows infected with S. aureus at 0, 1, 3, 5, and 7 days.
Results: Ttal of 288 differentially expressed miRNAs (DIE-miRNA) including 108 known and 180 novel predicted miRNAs, involved in 10 immune system-related signaling pathways. Compare with the 0 dpi, the number of DIE-miRNAs in 1, 3, 5, and 7 dpi groups were 12, 21, 75, and 48, respectively. It was also found that the expression variation of up-regulated expression of miR-320a, miR-19a, and miR-19b as well as down-regulated expression of miR-143, miR‑205, and miR‑24 reached a significant level on the 5 dpi and 7 dpi. However, at different times after S. aureus infection, miR-1301 was significantly up-regulated in peripheral blood. miR-2284r was significantly down-regulated.
Conclusion: miR-1301 and miR-2284r might be the new blood biomarkers for S. aureus-infected dairy cow mastitis. The above results laid a new foundation for the research and development of molecular diagnosis and biological therapy technology for S. aureus-infected mastitis in dairy cow.

overall_design: The experimental animals in this study were lactating 2 to 3-year-old half-sib Chinese Holstein cows, which were obtained from a farm in Yangling, Shaanxi, China. They had the same feeding and management environment. The body conditions of the dairy cows were measured three weeks before the experiment. All individuals had no symptoms of mastitis, and the somatic cell count (SCC) of milk was less than 200,000/mL. The udders and mammilla of the experimental dairy cows were cleaned and sterilized with 75% ethanol, and 5 mL of 10^5 CFU/mL S. aureus (ATCC 25923) suspension was injected into the udders of the experimental dairy cows through the mammary duct with a milk-passing needle. On the 7th day of induction, the mammary gland tissues were collected using painless surgery for hematoxylin-eosin (HE) staining and pathological analysis for mastitis model identification. On the day 0 (control), 1, 3, 5, and 7 after S. aureus infection, peripheral blood was collected from the jugular vein, and blood samples of different individuals with the same induction time were mixed and used to perform RNAseq.

first: Zhuo-Ma

last: LuoReng

first: Lin-Sen

last: Zan


title: Sequencing of human breast cancer cell line MDA-MB-231 and its highly pulmonary metastatic subline MDA-MB-231-LM2

city: Xuzhou

first: Chen-Long

state: Jiangsu

address: No. 209 Tongshan Rd.

institute: Xuzhou Medical University

summary:
Purpose: Tumor metastasis is the main cause of death from breast cancer patients and cell migration plays a critical role in metastasis. Recent studies have shown long non-coding RNAs (lncRNAs) play an essential role in the initiation and progression of cancer. In the present study, the role of a LncRNA, Rho GTPase Activating Protein 5- Antisense 1 (ARHGAP5-AS1) in breast cancer was investigated.
Methods: RNA sequencing was performed to find out dysregulated LncRNAs in MDA-MB-231-LM2 cells. Transwell migration assays and F-actin staining were utilized to estimate cell migration ability. RNA pulldown assays and RNA immunoprecipitation were used to prove the interaction between ARHGAP5-AS1 and SMAD7. Western blot and immunofluorescence imaging were used to examine the protein levels. Dual luciferase reporter assays were performed to evaluate the activation of TGF-β signaling.
Results: Compared to MDA-MB-231 cells, the expression of LncRNA ARHGAP5-AS1 (NR_027263) was significantly suppressed in its highly metastatic subtype MDA-MB-231-LM2 cells. Functional study showed ARHGAP5-AS1 could inhibit cell migration via suppression of stress fibers in breast cancer cell lines. Afterwards, SMAD7 was further identified to interact with ARHGAP5-AS1 by its PY motif and thus its ubiquitination and degradation was blocked due to reduced interaction with E3 ligase SMURF1 and SMURF2. Moreover, ARHGAP5-AS1 could inhibit TGF-β signaling pathway due to its inhibitory role on SMAD7.
Conclusion: Overall, these findings demonstrate that ARHGAP5-AS1 inhibits breast cancer cell migration and could serve as a novel biomarker for breast cancer metastasis and a potent target for the treatment in the future.

overall_design: Whole RNA profiles of MDA-MB-231 and MDA-MB-231-LM2 cells.

first: Chen


title: Drug repurposing identifies a synergistic high-order drug combination to treat sunitinib-resistant renal cell carcinoma

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

institute: University of Geneva

summary: We report that in response to combination treatment with a synergistic low-dose four-drug combination, human Caki-1 cells resistant to sunitinib alter their pheno- and genotype. We detected that the metabolism of these cells is altered. Gene expression analysis revealed significant differential expression of genes related to mitosis, apoptosis and cell attachment. We detected regulation changes in enzymes mediating the ceramide and sphingolipid metabolism.

overall_design: The experiments have been designed to analyze the effect of a multidrug combination consisting of Rapta-C, erlotinib, metformin and parthenolide in the human Caki-1 cell line resistant to treatment with the small molecule-based targeted drug sunitinib.

first: Magdalena

last: Rausch

first: Adriano

last: Rutz

first: Pierre-Marie

last: Allard

first: Céline

last: Delucinge-Vivier

first: Myléne

last: Docquier

first: Olivier

last: Dormond

first: Paul

last: Dyson

first: Jean-Luc

last: Wolfender

first: Patrycja

last: Nowak-Sliwinska


title: Next Generation Sequencing Analysis of human pluripotent stem cells derived endothelial and smooth muscle cells

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary:
Purpose: global gene expression profiling of H1 and iPSC derived endothelial cells (ECs) and smooth mucle cells (SMCs).
Methods: SMART-seq2 amplified polyA RNA from undifferentiated H1 cells and iPSCs (in biological duplicates), cardiovascular progenitor cells, endothelial cells (ECs) and smooth muscle cells (SMCs)
Results: Insulin free condition promoted cardiovascular mesoderm, endothelial and smooth muscle differentiation.
Conclusions: the gene expression profiles of ECs and SMCs differentiated in insulin free medium confirmed that they are true ECs and SMCs.

overall_design: Perform RNA-seq of undifferentaited H1 and human iPSCs,  day 3 mesoderm progenitor cells, day 8 endothelial and smooth muscle cells.

first: Fengzhi

last: Zhang

first: Rujin

last: Huang


title: A 3D renal proximal tubule on chip model phenocopies Lowe  syndrome and Dent II disease tubulopathy.

city: Sheffield

first: Dr. Kai

last: Erdmann

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary: Lowe syndrome and Dent II disease are X-linked monogenetic diseases characterised  by a renal reabsorption defect in the proximal tubules and caused by mutations in the OCRL gene,  which codes for an inositol-5-phosphatase. The life expectancy of patients suffering from Lowe  syndrome is largely reduced because of the development of chronic kidney disease and related  complications. There is a need for physiological human in-vitro models for Lowe syndrome/Dent II  disease to study underpinning disease mechanisms and to identify and characterise potential  drugs and drug targets. Here we describe a proximal tubule organ on chip model combining 3D  tubule architecture with fluid flow shear stress, which phenocopies hallmarks of Lowe  syndrome/Dent II disease. We demonstrate the principal suitability of our in-vitro model for drug  target validation. Furthermore, using this model we demonstrate that proximal tubule cells lacking  OCRL expression upregulate markers typical for epithelial-mesenchymal transition (EMT)  including the transcription factor SNAI2/Slug and show increased collagen expression and  deposition, which potentially contributes to interstitial fibrosis and disease progression as observed  in Lowe syndrome and Dent II disease.

overall_design: Differential gene expression analysis between OCRL KO_HK2 cells (2 cell lines) vs WT HK2 cells cultured in 3D tubule architecture with fluid flow applying shear stress.

first: Sindhu

last: Naik

first: Maté

last: Ongenaert

first: Kai


title: Ciliogenesis and autophagy are coordinately regulated by EphA2 in the cornea to maintain proper epithelial architecture

status: Public on May 19 2021

first: Han

last: Peng

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

summary: Purpose: To understand the relationship between ciliogenesis and autophagy in the corneal epithelium.   Methods: siRNAs for EphA2 or PLD1 were used to inhibit protein expression in vitro. Morpholino-anti-EphA2 was used to knockdown EphA2 in Xenopus skin. An EphA2 knockout mouse was used to conduct loss of function studies. Autophagic vacuoles were visualized by contrast light microscopy. Autophagy flux, was measured by LC3 turnover and p62 protein levels. Immunostaining and confocal microscopy were conducted to visualize cilia in cultured cells and in vivo.  Results: Loss of EphA2 (i) increased corneal epithelial thickness by elevating proliferative potential in wing cells, (ii) reduced the number of ciliated cells, (iii) increased large hollow vacuoles, that could be rescued by BafA1; (iv) inhibited autophagy flux and (v) increased GFP-LC3 puncta in the mouse corneal epithelium. This indicated a role for EphA2 in stratified epithelial assembly via regulation of proliferation as well as a positive role in both ciliogenesis and end-stage autophagy. Inhibition of PLD1, an EphA2 interacting protein that is a critical regulator of end-stage autophagy, reversed the accumulation of vacuoles, and the reduction in the number of ciliated cells due to EphA2 depletion, suggesting EphA2 regulation of both end-stage autophagy and ciliogenesis via PLD1. PLD1 mediated rescue of ciliogenesis by EphA2 depletion was blocked by BafA1, placing autophagy between EphA2 signaling and regulation of ciliogenesis.   Conclusion: Our findings demonstrate a novel role for EphA2 in regulating both autophagy and ciliogenesis, processes that are essential for proper corneal epithelial homeostasis.  Purpose: To understand the relationship between ciliogenesis and autophagy in the corneal epithelium.   Methods: siRNAs for EphA2 or PLD1 were used to inhibit protein expression in vitro. Morpholino-anti-EphA2 was used to knockdown EphA2 in Xenopus skin. An EphA2 knockout mouse was used to conduct loss of function studies. Autophagic vacuoles were visualized by contrast light microscopy. Autophagy flux, was measured by LC3 turnover and p62 protein levels. Immunostaining and confocal microscopy were conducted to visualize cilia in cultured cells and in vivo.  Results: Loss of EphA2 (i) increased corneal epithelial thickness by elevating proliferative potential in wing cells, (ii) reduced the number of ciliated cells, (iii) increased large hollow vacuoles, that could be rescued by BafA1; (iv) inhibited autophagy flux and (v) increased GFP-LC3 puncta in the mouse corneal epithelium. This indicated a role for EphA2 in stratified epithelial assembly via regulation of proliferation as well as a positive role in both ciliogenesis and end-stage autophagy. Inhibition of PLD1, an EphA2 interacting protein that is a critical regulator of end-stage autophagy, reversed the accumulation of vacuoles, and the reduction in the number of ciliated cells due to EphA2 depletion, suggesting EphA2 regulation of both end-stage autophagy and ciliogenesis via PLD1. PLD1 mediated rescue of ciliogenesis by EphA2 depletion was blocked by BafA1, placing autophagy between EphA2 signaling and regulation of ciliogenesis.   Conclusion: Our findings demonstrate a novel role for EphA2 in regulating both autophagy and ciliogenesis, processes that are essential for proper corneal epithelial homeostasis.

overall_design: WT and EphA2-/- corneal epithelial layers were isolated as before. Total RNA from these epithelial sheets was isolated using miRNeasy Mini kit (RNeasy; Qiagen, Valencia, CA), RNAseq analysis was performed by the NUseq core using Illumina HiSeq  platform.

first: Nihal

last: Kaplan

first: Robert

last: Lavker


title: Effect of caboznatinib on transcriptome and signaling pathways in leukemic cell line K562

city: Taipei

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

institute: National Taiwan University

summary: To identify molecular effects of the tyrosine kinase inhibitor cabozantinib (XL184), we applied gene expression profiling in human erythroid leukemic cell lines K562 using Whole Transcriptome Shotgun Sequencing (RNA-seq). After K562 cell were treated with 1uM cabozantinib for 48 h, differentially expressed genes (DEGs) of 241 genes upregulated and 569 were downregulated were found compared with vehicle group. Up-regulated genes enriched in erythroid maturation associated pathways, such as heme metabolism, transcription factor GATA1 targets, and globin synthesis, while those genes downregulated after expose to cabozantinib were enriched in pathways involved in cell proliferation and cell survival function.

overall_design: Gene expression in K562 was measured after exposure for 48 h to 1uM cabozantinib (XL184) or to the vehicle control (DMSO).

first: Da-Liang

last: Ou

first: Liang-In

last: Lin


title: BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia [single-cell RNA-seq]

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Institute

summary: Hijacking of primitive hematopoietic enhancers, or generation of a neo-enhancer by genomic amplification, results in deregulation of BCL11B as the defining feature of a subset of T/myeloid leukemia.  We report H3K27ac and BCL11B binding in these Leukemias.

overall_design: Single cell RNAseq using 10X 3' v3.1

first: Lindsey

last: Montefiori

first: Charles

last: Mullighan


title: BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia  [single-cell multiomics]

overall_design: Single cell multiomics using 10X Single Cell ATAC + Gene Expression


title: Transcriptomic changes in macrophages induced by damage-associated molecular patterns (DAMPs)

city: Meguro-ku, Tokyo

first: Sho

last: Hangai

institute: The University of Tokyo

summary:
Dead cell-derived molecules, typically called as damage-accociated molecular patterns (DAMPs), have been shown to evoke inflammatory responses. Accordingly, it becomes increasingly clear that DAMPs play important role in pathogenesis of multiple diseases including inflammatory diseases and cancer.
To get a comprihensive view of DAMP-mediated inflammatory responses, we perfomed microarray analysis on murine macrophages treated by dead cell-derived molecules.

overall_design: Mouse peritoneal macrophages (PECs) were treated by necrotic cell-derived supernatant for 2 hours. Subsequently, PECs were subjected to RNA extraction and hybridization to Clariom S array, Mouse.

first: Tadatsugu

last: Taniguchi

first: Hideyuki

last: Yanai


title: Chromatin assembly factor 1B critically controls early development but not functional acquisition of iNKT cells [ATAC-seq]

first: Yu

last: Xu

overall_design:
DP thymocytes of wild type (WT) and Chaf1b-deficient (KO) mice were analyzed chromatin accessibility by ATAC-seq with two replications.
Please note that each processed data file was generated from both replicates and is linked to the corresponding first replicate (*repeat1) sample records.

first: Junwei

last: Ma

first: Haorui

last: Luo

first: Yaohuang

last: Shi

first: Haifeng

last: Liu

first: Ao

last: Sun

first: Xiaolong


title: Resveratrol ameliorates lipid accumulation and inflammation in human SZ95 sebocytes via the AMPK signaling pathways in vitro

city: Nanjing

first: Ziyu

last: Wei

address: Pujian Road 160, Shanghai

department: Genetic Skin Disease Center

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Background: Acne Vulgaris is one of the commonest dermatological challenges lacking effective and well-tolerated treatment. An earlier study indicated that resveratrol (RVT) exhibits therapeutic effects in patients with acne through unknown mechanisms.  Objectives: To evaluate the effects of RVT on linoleic acid (LA)-induced lipogenesis and peptidoglycan (PGN)-induced inflammation in cultured SZ95 sebocytes in vitro and to study the underlying mechanisms. Methods: Whole transcriptome analysis was performed with RNA-sequencing. Intracellular neutral lipids were detected by Nile red staining. Lipidomics was used to examine the changes of lipid profile in sebocytes. Interleukin (IL)-1β and IL-6 mRNA and protein levels were assessed by quantitative real-time PCR and Enzyme-Linked Immunosorbent Assay, respectively. Expressions of lipogenesis-related proteins inflammatory signaling pathway and AMP-activated protein kinase (AMPK) pathway were evaluated by Western blot. Specific small interfering RNA (siRNA) was used to knockdown sirtuin-1 (SIRT1) expression. Results: RVT suppressed lipogenesis-related pathway and nuclear factor-kappa B (NF-κB) signaling pathway, decreased the contents of unsaturated fatty acids in SZ95 sebocytes. LA-induced lipogenesis and the expression of lipid-related proteins were all downregulated by RVT. Besides, RVT promoted SIRT1 expression as well as the deacetylation of NF-κB p65 subunit, and subsequently reduced IL-1β and IL-6 secretion under PGN induction. Furthermore, RVT-mediated sebosuppressive and anti-inflammation effects were abolished by pretreatment with AMPK inhibitor Compound C, meanwhile, SIRT1 silencing abrogated the anti-inflammatory capacity of RVT. Conclusions: RVT exhibits sebosuppressive and anti-inflammatory effects in human sebocytes partially via the AMPK pathway, which may justify the role of RVT treatment in acne vulgaris.

overall_design: Examination of whole transcriptome expression in human SZ95 sebocytes treated with PGN, PGN+RVT,LA, LA+RVT. Three biological replicates were used for each group.

first: Qiang

last: Ju